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<html> <head> <title>MayaChemTools:Code:MolFilesToSD.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MolFilesToSD.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> 5 <span class="c"># $Revision: 1.38 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 38 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> 40 41 <span class="c"># Autoflush STDOUT</span> 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 43 44 <span class="c"># Starting message...</span> 45 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span> 46 <span class="k">print</span> <span class="q">"\n$ScriptName:Starting...\n\n"</span><span class="sc">;</span> 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 48 49 <span class="c"># Get the options and setup script...</span> 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> 53 <span class="s">}</span> 54 55 <span class="k">my</span><span class="s">(</span><span class="i">@MOLFilesList</span><span class="s">)</span><span class="sc">;</span> 56 <span class="i">@MOLFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"mol"</span><span class="s">)</span><span class="sc">;</span> 57 58 <span class="c"># Process options...</span> 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 62 63 <span class="k">print</span> <span class="q">"Generating SD file $OptionsInfo{SDFile}...\n"</span><span class="sc">;</span> 64 <span class="i">GenerateSDFile</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 65 66 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 67 68 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 69 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> 70 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 71 72 <span class="c">###############################################################################</span> 73 74 <span class="c"># Generate a SD file using all valid MDL MOL files...</span> <a name="GenerateSDFile-"></a> 75 <span class="k">sub </span><span class="m">GenerateSDFile</span> <span class="s">{</span> 76 <span class="k">my</span><span class="s">(</span><span class="i">$MOLFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileCount</span><span class="cm">,</span> <span class="i">$FileOkayCount</span><span class="cm">,</span> <span class="i">$MolNameLine</span><span class="cm">,</span> <span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span><span class="sc">;</span> 77 78 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">">$OptionsInfo{SDFile}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $OptionsInfo{SDFile}: $! \n"</span><span class="sc">;</span> 79 <span class="i">$FileCount</span> = <span class="n">0</span><span class="sc">;</span> 80 <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span> 81 82 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#MOLFilesList</span><span class="s">)</span> <span class="s">{</span> 83 <span class="i">$MOLFile</span> = <span class="i">$MOLFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 84 <span class="i">$FileCount</span>++<span class="sc">;</span> 85 86 <span class="k">print</span> <span class="q">"Processing file $MOLFile...\n"</span><span class="sc">;</span> 87 88 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$MOLFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 89 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $MOLFile: It doesn't exist\n"</span><span class="sc">;</span> 90 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 91 <span class="s">}</span> 92 93 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$MOLFile</span><span class="cm">,</span> <span class="q">"mol"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 94 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $MOLFile: It's not a MDLMOL file\n"</span><span class="sc">;</span> 95 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 96 <span class="s">}</span> 97 98 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">MOLFILE</span><span class="cm">,</span> <span class="q">"$MOLFile"</span><span class="s">)</span> <span class="s">{</span> 99 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $MOLFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 100 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 101 <span class="s">}</span> 102 103 <span class="i">$FileOkayCount</span>++<span class="sc">;</span> 104 105 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyData</span>}<span class="s">)</span> <span class="s">{</span> 106 <span class="i">$MolNameLine</span> = <span class="q"><MOLFILE></span><span class="sc">;</span> 107 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseFilePrefix</span>}<span class="s">)</span> <span class="s">{</span> 108 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$MOLFile</span><span class="s">)</span><span class="sc">;</span> 109 <span class="i">$CmpdID</span> = <span class="i">$FileName</span><span class="sc">;</span> 110 <span class="s">}</span> 111 <span class="k">else</span> <span class="s">{</span> 112 <span class="i">$CmpdID</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} . <span class="q">"$FileCount"</span><span class="sc">;</span> 113 <span class="s">}</span> 114 115 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddMolNameLine</span>}<span class="s">)</span> <span class="s">{</span> 116 <span class="k">print</span> <span class="i">SDFILE</span> <span class="q">"$CmpdID\n"</span><span class="sc">;</span> 117 <span class="s">}</span> 118 <span class="k">else</span> <span class="s">{</span> 119 <span class="i">$MolNameLine</span> =~ <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span> 120 <span class="k">print</span> <span class="i">SDFILE</span> <span class="i">$MolNameLine</span><span class="sc">;</span> 121 <span class="s">}</span> 122 123 <span class="k">while</span> <span class="s">(</span><span class="q"><MOLFILE></span><span class="s">)</span> <span class="s">{</span> 124 <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span> 125 <span class="k">print</span> <span class="i">SDFILE</span><span class="sc">;</span> 126 <span class="s">}</span> 127 128 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddDataField</span>}<span class="s">)</span> <span class="s">{</span> 129 <span class="k">print</span> <span class="i">SDFILE</span> <span class="q">"> <$OptionsInfo{DataFieldLabel}>\n${CmpdID}\n"</span><span class="sc">;</span> 130 <span class="s">}</span> 131 <span class="s">}</span> 132 <span class="k">else</span> <span class="s">{</span> 133 <span class="k">while</span> <span class="s">(</span><span class="q"><MOLFILE></span><span class="s">)</span> <span class="s">{</span> 134 <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span> 135 <span class="k">print</span> <span class="i">SDFILE</span><span class="sc">;</span> 136 <span class="s">}</span> 137 <span class="s">}</span> 138 <span class="k">print</span> <span class="i">SDFILE</span> <span class="q">"\n\$\$\$\$\n"</span><span class="sc">;</span> 139 <span class="k">close</span> <span class="w">MOLFILE</span><span class="sc">;</span> 140 <span class="s">}</span> 141 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 142 143 <span class="k">print</span> <span class="q">"\nNumber of files: $FileCount\n"</span><span class="sc">;</span> 144 <span class="k">print</span> <span class="q">"Number of files processed successfully: $FileOkayCount\n"</span><span class="sc">;</span> 145 <span class="k">print</span> <span class="q">"Number of files ignored: "</span> . <span class="s">(</span><span class="i">$FileCount</span> - <span class="i">$FileOkayCount</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span> 146 <span class="s">}</span> 147 148 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 149 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 150 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 151 152 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 153 154 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span> 155 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldLabel</span>} = <span class="i">$Options</span>{<span class="w">datafieldlabel</span>}<span class="sc">;</span> 156 157 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 158 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 159 160 <span class="i">$OptionsInfo</span>{<span class="w">AddMolNameLine</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(molnameline|both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 161 <span class="i">$OptionsInfo</span>{<span class="w">AddDataField</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(datafield|both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 162 163 <span class="i">$OptionsInfo</span>{<span class="w">AddMolNameLine</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(molnameline|both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 164 <span class="i">$OptionsInfo</span>{<span class="w">AddDataField</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(datafield|both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 165 166 <span class="i">$OptionsInfo</span>{<span class="w">ModifyData</span>} = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddMolNameLine</span>} || <span class="i">$OptionsInfo</span>{<span class="w">AddDataField</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 167 168 <span class="i">$OptionsInfo</span>{<span class="w">UseFilePrefix</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundid</span>} =~ <span class="q">/^usefileprefix$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 169 170 <span class="c"># Setup SD file name...</span> 171 <span class="k">my</span><span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 172 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span> 173 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 174 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span> 175 <span class="k">if</span> <span class="s">(</span><span class="i">$FileName</span> && <span class="i">$FileExt</span><span class="s">)</span> <span class="s">{</span> 176 <span class="i">$SDFile</span> = <span class="i">$FileName</span><span class="sc">;</span> 177 <span class="s">}</span> 178 <span class="k">else</span> <span class="s">{</span> 179 <span class="i">$SDFile</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span> 180 <span class="s">}</span> 181 <span class="i">$SDFile</span> .= <span class="q">".sdf"</span><span class="sc">;</span> 182 <span class="s">}</span> 183 <span class="k">else</span> <span class="s">{</span> 184 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 185 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$MOLFilesList</span>[<span class="n">0</span>]<span class="s">)</span><span class="sc">;</span> 186 <span class="i">$SDFile</span> = <span class="i">$FileName</span> . <span class="q">"1To"</span> . <span class="i">@MOLFilesList</span> . <span class="q">".sdf"</span><span class="sc">;</span> 187 <span class="s">}</span> 188 189 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span> 190 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span> <span class="s">{</span> 191 <span class="k">die</span> <span class="q">"Error: The file $SDFile already exists.\n"</span><span class="sc">;</span> 192 <span class="s">}</span> 193 <span class="s">}</span> 194 <span class="i">$OptionsInfo</span>{<span class="w">SDFile</span>} = <span class="i">$SDFile</span><span class="sc">;</span> 195 196 <span class="s">}</span> 197 198 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 199 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 200 201 <span class="c"># Retrieve all the options...</span> 202 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 203 <span class="i">$Options</span>{<span class="w">compoundid</span>} = <span class="q">"Cmpd"</span><span class="sc">;</span> 204 <span class="i">$Options</span>{<span class="w">datafieldlabel</span>} = <span class="q">"Cmpd_ID"</span><span class="sc">;</span> 205 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"none"</span><span class="sc">;</span> 206 207 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"compoundid|c=s"</span><span class="cm">,</span> <span class="q">"datafieldlabel|d=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 208 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 209 <span class="s">}</span> 210 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 211 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 212 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 213 <span class="s">}</span> 214 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 215 <span class="s">}</span> 216 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(molnameline|datafield|both|none)$/i</span> <span class="s">)</span> <span class="s">{</span> 217 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molnameline, datafield, both, or none\n"</span><span class="sc">;</span> 218 <span class="s">}</span> 219 <span class="s">}</span> 220 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>